Ccp4 ncont

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Type Python Script
Download ccp4_ncont.py
Author(s) Gerhard Reitmayr and Dalia Daujotyte
License GPL
This code has been put under version control in the project Pymol-script-repo

Contents

Overview

Interface residues (at cutoff <4A) in the 2c7r.pdb were found using NCONT. Usage of ccp4_ncont script in PyMOL allows easy selection of residues and atoms listed in ncont.log file. Interacting protein and DNA residues are colored in red and slate, respectively. Atoms in contact are shown in dots.

The script selects residues and atoms from the list of the contacts found by NCONT from CCP4 Program Suite (NCONT analyses contacts between subsets of atoms in a PDB file). First, we run NCONT on our pdb file to find interface residues. Then by using the ccp4_ncont script in PyMOL we separately select residues and atoms listed in a ncont.log file. This generates two selections (atoms and residues) for each interacting chain, allowing quick manipulation of (sometimes) extensive lists in NCONT log file.

This script works best for intermolecular contacts (when NCONT target and source selections don't overlap). If crystal contacts (NCONT parameter cell = 1 or 2) are included then additional coding is required to distinguish inter from intramolecular contacts.

Usage

ccp4_ncont( contactsfile, selName1 = "source", selName2 = "target" )


Examples

First use NCONT to find interface residues/atoms in the pdb file. Once you have ncont.log file proceed to PyMOL. Make sure you import the ccp4_ncont script first.

fetch 2c7r
ccp4_ncont 2c7r.ncont, selName1=prot, selName2=dna
Quick and easy selection of interacting residues and atoms listed in the NCONT log file. Protein and DNA residues are colored in red and slate, respectively. Atoms in contact are shown in dots.
Download: examples/ccp4_ncont_1.pml
This code has been put under version control in the project Pymol-script-repo
reinitialize
import ccp4_ncont
 
fetch 2c7r, async=0
remove solvent
show_as cartoon, 2c7r
 
python
if 'PYMOL_GIT_MOD' in os.environ:
    example_dir = os.path.join(os.path.split(os.environ['PYMOL_GIT_MOD'])[0],"files_for_examples")
    ncontfile = os.path.join(example_dir,"2c7r.ncont")
else:
    ncontfile = "2c7r.ncont"
python end
 
select ligands, organic
select prot, chain A
select ssDNAa, chain C
select ssDNAb, chain D
select dsDNA, chain C+D
 
ccp4_ncont.ccp4_ncont(ncontfile, selName1="prot", selName2="dsDNA")
 
# See here to represent nuc acids
#http://www.pymolwiki.org/index.php/Examples_of_nucleic_acid_cartoons
set cartoon_ring_mode, 3
set cartoon_ring_finder, 1
color slate, dsDNA and elem C
 
show sticks, prot_res
color raspberry, prot_res
show dots,  prot_atom
show dots, dsDNA_atom
orient dsDNA_res
ray
 

Getting a NCONT file

Install CCP4 - for Linux

Goto: http://www.ccp4.ac.uk/download.php
Click: automated Downloads Pages
Select: Linux, generic linux (x86)
Select: Customized installation
Select: Only CCP4 Program Suite, Executables -> Continue
No additional packages -> Continue
Download

Extract for example to: /home/YOU/Software/CCP4
Then run:

$ /home/YOU/Software/CCP4/install.sh

write yes, read agreement, push y to agree license
For sourcing scripts, say yes.
See the changes to your environmental virables:

$ less ~/.bashrc

Use of NCONT - for Linux

See here for the NCONT program and options:
http://www.ccp4.ac.uk/html/ncont.html
http://www.ccp4.ac.uk/html/pdbcur.html#atom_selection
Locate the pdb, and now run in terminal:

$ ncont XYZIN 2c7r.pdb >> 2c7r.ncont << eof   (#press enter)
> source A    (#press enter)
> target C,D  (#press enter)
> eof         (#press enter, and now the program runs, and shell saves to 2c7r.ncont)
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